Dental calculus, the mineralised plaque that dentists scrape away, is for archaeologists a time capsule: it entombs the DNA of the microbes that lived in a person's mouth. Researchers at the University of Tokyo, working with colleagues led from Toho University, analysed DNA preserved in calculus from ancient skeletons of the Japanese archipelago, principally from the Edo period, to reconstruct oral microbiomes of the past.
The comparison with modern samples showed that ancient oral microbial communities differed from those of today, with regional variation and bacterial lineages that distinguish Jomon-period from Edo-period individuals. A phylogenetic analysis of Methanobrevibacter oralis, an archaeon associated with periodontal disease, found that strains from female individuals bearing traces of tooth blackening, a cosmetic practice of the era, fell into a single evolutionary clade.
Published in Scientific Reports, the work demonstrates that microbial DNA locked in calculus can speak to past diets, regional lifeways and even cosmetic customs, alongside the long co-evolutionary history between humans and the microbes that live with them. For historians and archaeologists of pre-modern Japan, it adds a molecular dimension to the study of everyday life, recoverable from skeletal material that museums already hold.